Background: The present study investigated whether the frequency-following response (FFR) of the auditory brainstem can represent individual frequency-discrimination ability. Method: We measured behavioral frequency-difference limens (FDLs) in normal hearing young adults. Then FFRs were evoked by two pure tones, whose frequency difference was no larger than behavioral FDL. Discrimination of FFRs to individual frequencies was conducted as the neural representation of stimulus frequency difference. Participants were 15 Chinese college students (ages 19–25; 3 males, 12 females) with normal hearing characteristics. Results: According to discriminative neural representations of individual frequencies, FFRs accurately reflected individual FDLs and detected stimulus-frequency differences smaller than behavioral threshold (e.g., 75% of FDL). Conclusions: These results suggest that when a frequency difference cannot be behaviorally distinguished, there is still a possibility of it being detected physiologically.